docs: def _get_assembled_reference_sequences(nucmer_hits, ref_sequence, assembly):
          '''nucmer_hits =  hits made by self._parse_nucmer_coords_file.
             ref_gene = reference sequence (pyfastaq.sequences.Fasta object)
             assembly = dictionary of contig name -> contig.
             Makes a set of Fasta objects of each piece of assembly that
             corresponds to the reference sequeunce.'''
          sequences = {}
  
          for contig in sorted(nucmer_hits):
              for hit in nucmer_hits[contig]:
                  qry_coords = hit.qry_coords()
                  fa = assembly[hit.qry_name].subseq(qry_coords.start, qry_coords.end + 1)
                  if hit.on_same_strand():
                      strand = '+'
                  else:
                      fa.revcomp()
                      strand = '-'
                  ref_coords = hit.ref_coords()
                  fa.id = '.'.join([
                      ref_sequence.id,
                      str(ref_coords.start + 1),
                      str(ref_coords.end + 1),
                      contig,
                      str(qry_coords.start + 1),
                      str(qry_coords.end + 1),
                      strand
                  ])
  
                  if hit.hit_length_ref == hit.ref_length:
                      fa.id += '.complete'
  
                  sequences[fa.id] = fa
  
          return sequences